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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaaatatttggcatagtacgttgttgtgggccgggtgaattttgttaaaactttgcagttcatgttatagtggatttagttgattttcttttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAAGCTATTGGCTCTATCATTACTAACACTCGGAATGAAGGATATCCCGGTG

Basic information

species Glycine max
transcript GLYMA09G33480.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0211g00160.t01 (Vitis vinifera), 3'ss of exon 3
---tgaaatatttggcatagtacgttgttgtgggccgggtgaattttgttaaaactttgcagttcatgtt-atagtggatttagttgattttcttttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAAGCTATTGGCTCTATCATTACTAACACTCGGAATGAAGGATATCCCGGTG
   |||| | ||  ||||||     | ||  |   ||  |   ||  |||    |||||  || || ||| |||    | | |     |||| | || || |||||||| ||||| |||||||||||||| ||||||||||| || || ||||||||| |||| ||||| || || ||||     |  ||||||||||| || |
acttgaatttttcagcatagattccttttcggcatcgatt---ttgagttggtgctttgt-gtacaagttgatatcctactgaaaatcttttgtgtttgtaaagGGACTTGAACTCATACCCTCCGAGAACTTCACTTCTGTGTCAGTTATGCAAGCTGTTGGGTCTATTATGACAAACAAGTACAGCGAAGGATATCCAGGCG

upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 3
---tgaaatatttggcatagtacgttgttgtgggccgggtgaattttgttaaaactttgcagttcatgtt-atagtggatttagttgattttcttttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAAGCTATTGGCTCTATCATTACTAACACTCGGAATGAAGGATATCCCGGTG
   |||| | ||  ||||||     | ||  |   ||  |   ||  |||    |||||  || || ||| |||    | | |     |||| |  | || |||| ||| |||||  ||||||||||||| ||||||||||| || || ||||||||| |||| ||||| || || |||| |   |  ||||||||||| || |
acttgaatttttcagcatagattccttttcggcatcgatt---ttgagttggtgctttgt-gtacaagttgatatcctactgaaaatcttttgtgcttgtaaagGCACTTGAACTCGTACCCTCCGAGAACTTCACTTCTGTGTCAGTTATGCAAGCTGTTGGGTCTATTATGACAAACAATGTCAGCGAAGGATATCCAGGCG

upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 3
---tgaaatatttggcatagtacgttgttgtgggccgggtgaattttgttaaaactttgcagttcatgtt-atagtggatttagttgattttcttttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAAGCTATTGGCTCTATCATTACTAACACTCGGAATGAAGGATATCCCGGTG
   |||| | ||  ||||||     | ||  |   ||  |   ||  |||    |||||  || || ||| |||    | | |     |||| |  | || |||||||| ||||| |||||||||||||| ||||||||||| || || ||||||||| |||| ||||| || || ||||     |  ||||||||||| || |
acttgaatttttcagcatagattccttttcggcatcgatt---ttgagttggtgctttgt-gtacaagttgatatcctactgaaaatcttttgtgcttgtaaagGGACTTGAACTCATACCCTCCGAGAACTTCACTTCTGTGTCAGTTATGCAAGCTGTTGGGTCTATTATGACAAACAAGTACAGCGAAGGATATCCAGGCG

upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 3'ss of exon 3
---tgaaatatttggcatagtacgttgttgtgggccgggtgaattttgttaaaactttgcagttcatgtt-atagtggatttagttgattttcttttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAAGCTATTGGCTCTATCATTACTAACACTCGGAATGAAGGATATCCCGGTG
   |||| | ||  ||||||     | ||  |   ||  |   ||  ||     |||||  || || ||| |||    | | |     |||| |  | || |||| ||| |||||  ||||||||||||| ||||||||||| || || ||||||||| |||| ||||| || || |||| |   |  ||||||||||| || |
acttgaatttttcagcatagattccttttcggcatcgatt---ttgagtcggtgctttgt-gtacaagttgatatcctactgaaaatcttttgtgcttgtaaagGCACTTGAACTCGTACCCTCCGAGAACTTCACTTCTGTGTCAGTTATGCAAGCTGTTGGGTCTATTATGACAAACAATGTCAGCGAAGGATATCCAGGCG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|208263551|gb|GE063811.1|GE063811
EST:     CCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAG                         GGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
genomic: CCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAGgtatacataa ... tttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
EST: gi|208315715|gb|GE114785.1|GE114785
EST:     ACCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAG                         GGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
genomic: ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAGgtatacataa ... tttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
EST: gi|193401889|gb|FK367094.1|FK367094
EST:     ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAG                         GGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATAGCA
genomic: ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAGgtatacataa ... tttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAAT-GCA
EST: gi|193469321|gb|FK437627.1|FK437627
EST:     ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAG                         GGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
genomic: ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAGgtatacataa ... tttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
EST: gi|193588700|gb|FK540098.1|FK540098
EST:     GAAAAAGCTAGACAATGGAAG                         GGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
genomic: GAAAAAGCTAGACAATGGAAGgtatacataa ... tttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
EST: gi|207765710|gb|GD735955.1|GD735955
EST:     CCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAG                         GGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
genomic: CCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAGgtatacataa ... tttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
EST: gi|207789742|gb|GD763456.1|GD763456
EST:     ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAG                         GGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
genomic: ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAGgtatacataa ... tttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
EST: gi|193515317|gb|FK472879.1|FK472879
EST:     ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAG                         GGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
genomic: ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAGgtatacataa ... tttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
EST: gi|208303241|gb|GE101062.1|GE101062
EST:     ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAG                         GGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
genomic: ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAGgtatacataa ... tttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
EST: gi|208046547|gb|GD849103.1|GD849103
EST:     ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAG                         GGACTGGAACTGATACCCTCCGAGAATTTCA
genomic: ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAGgtatacataa ... tttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCA
EST: gi|193595490|gb|FK554355.1|FK554355
EST:     ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAG                         GGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
genomic: ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAGgtatacataa ... tttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
EST: gi|208172749|gb|GD969352.1|GD969352
EST:     ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAG                         GGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
genomic: ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAGgtatacataa ... tttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
EST: gi|207808489|gb|GD777662.1|GD777662
EST:     ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAG                         GGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
genomic: ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAGgtatacataa ... tttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
EST: gi|193471231|gb|FK438124.1|FK438124
EST:     ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAG                         GGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
genomic: ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAGgtatacataa ... tttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
EST: gi|208310329|gb|GE105549.1|GE105549
EST:     ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAG                         GGACTGGAACTGATACCCTCCGAGAATTCCACTTCTGTCTCTGTAATGCAA
genomic: ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAGgtatacataa ... tttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
EST: gi|193540875|gb|FK496051.1|FK496051
EST:     ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAG                         GGACTGGAACTGATACCCTCCGA
genomic: ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAGgtatacataa ... tttggtgaagGGACTGGAACTGATACCCTCCGA
EST: gi|193308001|gb|FK272023.1|FK272023
EST:     TAATTGAGCTTGAAAAAGCTAGACAATGGAAG                         GGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
genomic: TAATTGAGCTTGAAAAAGCTAGACAATGGAAGgtatacataa ... tttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAA
EST: gi|208138614|gb|GD939746.1|GD939746
EST:     ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAG                         GGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGT
genomic: ATCCTGAGATTGCTGATATAATTGAGCTTGAAAAAGCTAGACAATGGAAGgtatacataa ... tttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaactttgcagttcatgttatagtggatttagttgattttcttttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAAGCTATTGGCTCTATCATTACTAACACTCGGAATGAAGGATATCCCGGTG
                                 agttgat  putative branch site (score: 5)
                                       ttttctttt  CT-rich tract
                             atttagttgatttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaaatatttggcatagtacgttgttgtgggccgggtgaattttgttaaaactttgcagttcatgttatagtggatttagttgattttcttttggtgaagGGACTGGAACTGATACCCTCCGAGAATTTCACTTCTGTCTCTGTAATGCAAGCTATTGGCTCTATCATTACTAACACTCGGAATGAAGGATATCCCGGTG

- - - - - - - - - - - - ttgtggg
- - - - - - - - - - - - - - - - -gggtgaa
- - - - - - - - - - - - - - - - - - - - - - - - - -ctttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgtt